react-msaview 3.1.12 → 3.2.0

package/dist/components/msa/MSAMouseoverCanvas.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
-declare const MSAMouseoverCanvas: ({ model, }: {
+import type { MsaViewModel } from '../../model';
+declare const MSAMouseoverCanvas: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;
 export default MSAMouseoverCanvas;

package/dist/components/msa/MSAMouseoverCanvas.js

@@ -2,7 +2,7 @@ import React, { useEffect, useRef } from 'react';
 import { observer } from 'mobx-react';
 import { autorun } from 'mobx';
 import { renderMouseover } from './renderMSAMouseover';
-const MSAMouseoverCanvas = observer(function ({ model, }) {
+const MSAMouseoverCanvas = observer(({ model }) => {
     const ref = useRef(null);
     const { height, width } = model;
     useEffect(() => {

package/dist/components/msa/MSAMouseoverCanvas.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MSAMouseoverCanvas.js","sourceRoot":"","sources":["../../../src/components/msa/MSAMouseoverCanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAI9B,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AAEtD,MAAM,kBAAkB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACzE,MAAM,GAAG,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IAC3C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAC/B,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,EAAE,UAAU,CAAC,IAAI,CAAC,CAAA;QACzC,OAAO,GAAG;YACR,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE;gBACX,eAAe,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,CAAC,CAAA;YACjC,CAAC,CAAC;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAA;IAEX,OAAO,CACL,gCACE,GAAG,EAAE,GAAG,EACR,EAAE,EAAC,WAAW,EACd,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,CAAC;YACN,IAAI,EAAE,CAAC;YACP,KAAK;YACL,MAAM;YACN,MAAM,EAAE,IAAI;YACZ,aAAa,EAAE,MAAM;SACtB,GACD,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}

package/dist/components/msa/MSAPanel.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const MSAPanel: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/msa/renderBoxFeatureCanvasBlock.d.ts

@@ -1,4 +1,4 @@
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 export declare function renderBoxFeatureCanvasBlock({ model, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeYOverride, }: {
     offsetX: number;
     offsetY: number;

package/dist/components/msa/renderBoxFeatureCanvasBlock.js

@@ -1,12 +1,11 @@
 export function renderBoxFeatureCanvasBlock({ model, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeYOverride, }) {
-    const { hierarchy, blockSize, rowHeight, highResScaleFactor, showDomains } = model;
+    const { leaves, blockSize, rowHeight, highResScaleFactor, showDomains } = model;
     if (showDomains) {
         const k = highResScaleFactorOverride || highResScaleFactor;
         const by = blockSizeYOverride || blockSize;
         ctx.resetTransform();
         ctx.scale(k, k);
         ctx.translate(-offsetX, rowHeight / 2 - offsetY);
-        const leaves = hierarchy.leaves();
         const yStart = Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight));
         const yEnd = Math.max(0, Math.ceil((offsetY + by + rowHeight) / rowHeight));
         const visibleLeaves = leaves.slice(yStart, yEnd);

package/dist/components/msa/renderBoxFeatureCanvasBlock.js.map

@@ -1 +1 @@
-{"version":3,"file":"renderBoxFeatureCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/msa/renderBoxFeatureCanvasBlock.ts"],"names":[],"mappings":"AAMA,MAAM,UAAU,2BAA2B,CAAC,EAC1C,KAAK,EACL,OAAO,EACP,OAAO,EACP,GAAG,EACH,0BAA0B,EAC1B,kBAAkB,GAQnB;IACC,MAAM,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,kBAAkB,EAAE,WAAW,EAAE,GACxE,KAAK,CAAA;IACP,IAAI,WAAW,EAAE,CAAC;QAChB,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;QAC1D,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;QAC1C,GAAG,CAAC,cAAc,EAAE,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,SAAS,GAAG,CAAC,GAAG,OAAO,CAAC,CAAA;QAEhD,MAAM,MAAM,GAAG,SAAS,CAAC,MAAM,EAAE,CAAA;QACjC,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;QACzE,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;QAC3E,MAAM,aAAa,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAEhD,SAAS,CAAC;YACR,KAAK;YACL,GAAG;YACH,aAAa;SACd,CAAC,CAAA;IACJ,CAAC;AACH,CAAC;AAED,SAAS,SAAS,CAAC,EACjB,KAAK,EACL,GAAG,EACH,aAAa,GAKd;IACC,MAAM,EACJ,cAAc,EACd,QAAQ,EACR,SAAS,EACT,WAAW,EACX,aAAa,EACb,+BAA+B,GAChC,GAAG,KAAK,CAAA;IAET,KAAK,MAAM,IAAI,IAAI,aAAa,EAAE,CAAC;QACjC,MAAM,EACJ,CAAC,EACD,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;QACR,MAAM,CAAC,GAAG,CAAE,CAAA;QAEZ,MAAM,KAAK,GAAG,+BAA+B,EAAE,CAAC,IAAI,CAAC,CAAA;QAErD,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,KAAK,EAAE,CAAC;YACV,KAAK,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,IAAI,KAAK,EAAE,CAAC;gBAC9C,MAAM,EAAE,GAAG,KAAK,CAAC,gCAAgC,CAAC,IAAI,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;gBAClE,MAAM,EAAE,GAAG,KAAK,CAAC,gCAAgC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;gBAC5D,MAAM,CAAC,GAAG,EAAE,GAAG,QAAQ,CAAA;gBACvB,GAAG,CAAC,SAAS,GAAG,WAAW,CAAC,SAAS,CAAC,CAAA;gBACtC,GAAG,CAAC,WAAW,GAAG,aAAa,CAAC,SAAS,CAAC,CAAA;gBAC1C,MAAM,CAAC,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;gBACxC,MAAM,CAAC,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBACtD,MAAM,EAAE,GAAG,QAAQ,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,CAAA;gBAC/B,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;gBACzB,GAAG,CAAC,UAAU,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;gBAC3B,CAAC,EAAE,CAAA;YACL,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}
+{"version":3,"file":"renderBoxFeatureCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/msa/renderBoxFeatureCanvasBlock.ts"],"names":[],"mappings":"AAMA,MAAM,UAAU,2BAA2B,CAAC,EAC1C,KAAK,EACL,OAAO,EACP,OAAO,EACP,GAAG,EACH,0BAA0B,EAC1B,kBAAkB,GAQnB;IACC,MAAM,EAAE,MAAM,EAAE,SAAS,EAAE,SAAS,EAAE,kBAAkB,EAAE,WAAW,EAAE,GACrE,KAAK,CAAA;IACP,IAAI,WAAW,EAAE,CAAC;QAChB,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;QAC1D,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;QAC1C,GAAG,CAAC,cAAc,EAAE,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,SAAS,GAAG,CAAC,GAAG,OAAO,CAAC,CAAA;QAEhD,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;QACzE,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;QAC3E,MAAM,aAAa,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAEhD,SAAS,CAAC;YACR,KAAK;YACL,GAAG;YACH,aAAa;SACd,CAAC,CAAA;IACJ,CAAC;AACH,CAAC;AAED,SAAS,SAAS,CAAC,EACjB,KAAK,EACL,GAAG,EACH,aAAa,GAKd;IACC,MAAM,EACJ,cAAc,EACd,QAAQ,EACR,SAAS,EACT,WAAW,EACX,aAAa,EACb,+BAA+B,GAChC,GAAG,KAAK,CAAA;IAET,KAAK,MAAM,IAAI,IAAI,aAAa,EAAE,CAAC;QACjC,MAAM,EACJ,CAAC,EACD,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;QACR,MAAM,CAAC,GAAG,CAAE,CAAA;QAEZ,MAAM,KAAK,GAAG,+BAA+B,EAAE,CAAC,IAAI,CAAC,CAAA;QAErD,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,KAAK,EAAE,CAAC;YACV,KAAK,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,IAAI,KAAK,EAAE,CAAC;gBAC9C,MAAM,EAAE,GAAG,KAAK,CAAC,gCAAgC,CAAC,IAAI,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;gBAClE,MAAM,EAAE,GAAG,KAAK,CAAC,gCAAgC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;gBAC5D,MAAM,CAAC,GAAG,EAAE,GAAG,QAAQ,CAAA;gBACvB,GAAG,CAAC,SAAS,GAAG,WAAW,CAAC,SAAS,CAAC,CAAA;gBACtC,GAAG,CAAC,WAAW,GAAG,aAAa,CAAC,SAAS,CAAC,CAAA;gBAC1C,MAAM,CAAC,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;gBACxC,MAAM,CAAC,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBACtD,MAAM,EAAE,GAAG,QAAQ,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,CAAA;gBAC/B,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;gBACzB,GAAG,CAAC,UAAU,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;gBAC3B,CAAC,EAAE,CAAA;YACL,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/components/msa/renderMSABlock.d.ts

@@ -1,5 +1,5 @@
-import { Theme } from '@mui/material';
-import { MsaViewModel } from '../../model';
+import type { Theme } from '@mui/material';
+import type { MsaViewModel } from '../../model';
 export declare function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }: {
     offsetX: number;
     offsetY: number;

package/dist/components/msa/renderMSABlock.js

@@ -1,6 +1,6 @@
 import { getClustalXColor, getPercentIdentityColor } from '../../colorSchemes';
 export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
-    const { hierarchy, colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, showDomains, } = model;
+    const { colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, actuallyShowDomains, leaves, } = model;
     const k = highResScaleFactorOverride || highResScaleFactor;
     const bx = blockSizeXOverride || blockSize;
     const by = blockSizeYOverride || blockSize;
@@ -9,13 +9,12 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
     ctx.translate(-offsetX, rowHeight / 2 - offsetY);
     ctx.textAlign = 'center';
     ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
-    const leaves = hierarchy.leaves();
     const yStart = Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight));
     const yEnd = Math.max(0, Math.ceil((offsetY + by + rowHeight) / rowHeight));
     const xStart = Math.max(0, Math.floor(offsetX / colWidth));
     const xEnd = Math.max(0, Math.ceil((offsetX + bx) / colWidth));
     const visibleLeaves = leaves.slice(yStart, yEnd);
-    if (!showDomains) {
+    if (!actuallyShowDomains) {
         drawTiles({
             model,
             ctx,
@@ -40,7 +39,7 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
     ctx.resetTransform();
 }
 function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, }) {
-    const { bgColor, colorSchemeName, colorScheme, colStats, columns, colWidth, rowHeight, } = model;
+    const { bgColor, colorSchemeName, colorScheme, colStats, colStatsSums, columns, colWidth, rowHeight, } = model;
     for (const node of visibleLeaves) {
         const { data: { name }, } = node;
         const y = node.x;
@@ -48,21 +47,20 @@ function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, })
         for (let i = 0; i < str?.length; i++) {
             const letter = str[i];
             const color = colorSchemeName === 'clustalx_protein_dynamic'
-                ? getClustalXColor(colStats[xStart + i], model, name, xStart + i)
+                ? getClustalXColor(colStats[xStart + i], colStatsSums[xStart + i], model, name, xStart + i)
                 : colorSchemeName === 'percent_identity_dynamic'
-                    ? getPercentIdentityColor(colStats[xStart + i], model, name, xStart + i)
+                    ? getPercentIdentityColor(colStats[xStart + i], colStatsSums[xStart + i], model, name, xStart + i)
                     : colorScheme[letter.toUpperCase()];
             if (bgColor) {
-                const x = i * colWidth + offsetX - (offsetX % colWidth);
                 ctx.fillStyle = color || theme.palette.background.default;
-                ctx.fillRect(x, y - rowHeight, colWidth, rowHeight);
+                ctx.fillRect(i * colWidth + offsetX - (offsetX % colWidth), y - rowHeight, colWidth, rowHeight);
             }
         }
     }
 }
 function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart, xEnd, }) {
-    const { bgColor, showDomains, colorScheme, columns, colWidth, rowHeight } = model;
-    if (rowHeight >= 5 && colWidth > rowHeight / 2) {
+    const { bgColor, actuallyShowDomains, showMsaLetters, colorScheme, columns, colWidth, contrastLettering, rowHeight, } = model;
+    if (showMsaLetters) {
         for (const node of visibleLeaves) {
             const { data: { name }, } = node;
             const y = node.x;
@@ -70,10 +68,12 @@ function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart,
             for (let i = 0; i < str?.length; i++) {
                 const letter = str[i];
                 const color = colorScheme[letter.toUpperCase()];
-                const contrast = contrastScheme[letter.toUpperCase()] || 'black';
+                const contrast = contrastLettering
+                    ? contrastScheme[letter.toUpperCase()] || 'black'
+                    : 'black';
                 const x = i * colWidth + offsetX - (offsetX % colWidth);
                 // note: -rowHeight/4 matches +rowHeight/4 in tree
-                ctx.fillStyle = showDomains
+                ctx.fillStyle = actuallyShowDomains
                     ? 'black'
                     : bgColor
                         ? contrast

package/dist/components/msa/renderMSABlock.js.map

@@ -1 +1 @@
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package/dist/components/msa/renderMSAMouseover.d.ts

@@ -1,4 +1,4 @@
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 export declare function renderMouseover({ ctx, model, }: {
     ctx: CanvasRenderingContext2D;
     model: MsaViewModel;

package/dist/components/tree/TreeBranchMenu.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 interface Node {
     x: number;
     y: number;

package/dist/components/tree/TreeCanvas.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const TreeCanvas: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/tree/TreeCanvas.js

@@ -1,4 +1,5 @@
-import React, { useEffect, useRef, useState } from 'react';
+import React from 'react';
+import { useEffect, useRef, useState } from 'react';
 import { observer } from 'mobx-react';
 import TreeCanvasBlock from './TreeCanvasBlock';
 import { padding } from './renderTreeCanvas';
@@ -40,7 +41,8 @@ const TreeCanvas = observer(function ({ model }) {
             const distanceY = currY - prevY.current;
             if (distanceY) {
                 // use rAF to make it so multiple event handlers aren't fired per-frame
-                // see https://calendar.perfplanet.com/2013/the-runtime-performance-checklist/
+                // see
+                // https://calendar.perfplanet.com/2013/the-runtime-performance-checklist/
                 if (!scheduled.current) {
                     scheduled.current = true;
                     window.requestAnimationFrame(() => {
@@ -79,16 +81,15 @@ const TreeCanvas = observer(function ({ model }) {
             setMouseDragging(true);
         }
     }
-    // this local mouseup is used in addition to the global because sometimes
-    // the global add/remove are not called in time, resulting in issue #533
-    function mouseUp(event) {
-        event.preventDefault();
-        setMouseDragging(false);
-    }
-    function mouseLeave(event) {
-        event.preventDefault();
-    }
-    return (React.createElement("div", { ref: ref, onMouseDown: mouseDown, onMouseUp: mouseUp, onMouseLeave: mouseLeave, style: {
+    return (React.createElement("div", { ref: ref, onMouseDown: mouseDown, onMouseUp: event => {
+            // this local mouseup is used in addition to the global because
+            // sometimes the global add/remove are not called in time, resulting in
+            // issue #533
+            event.preventDefault();
+            setMouseDragging(false);
+        }, onMouseLeave: event => {
+            event.preventDefault();
+        }, style: {
             height,
             position: 'relative',
             width: treeWidth + padding,

package/dist/components/tree/TreeCanvas.js.map

@@ -1 +1 @@
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package/dist/components/tree/TreeCanvasBlock.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const TreeCanvasBlock: ({ model, offsetY, }: {
     model: MsaViewModel;
     offsetY: number;

package/dist/components/tree/TreeCanvasBlock.js

@@ -1,4 +1,5 @@
-import React, { useCallback, useEffect, useRef, useState } from 'react';
+import React from 'react';
+import { useCallback, useEffect, useRef, useState } from 'react';
 import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
 import { useTheme } from '@mui/material';

package/dist/components/tree/TreeCanvasBlock.js.map

@@ -1 +1 @@
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package/dist/components/tree/TreeNodeMenu.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const TreeMenu: ({ node, onClose, model, }: {
     node: {
         x: number;

package/dist/components/tree/TreeNodeMenu.js

@@ -4,7 +4,7 @@ import { observer } from 'mobx-react';
 // lazies
 const TreeNodeInfoDialog = lazy(() => import('./dialogs/TreeNodeInfoDialog'));
 const TreeMenu = observer(function ({ node, onClose, model, }) {
-    const { collapsed, collapsed2 } = model;
+    const { collapsed, collapsedLeaves } = model;
     return (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
             top: node.y,
             left: node.x,
@@ -35,7 +35,7 @@ const TreeMenu = observer(function ({ node, onClose, model, }) {
                     }
                 }
                 onClose();
-            } }, collapsed.includes(node.id) || collapsed2.includes(node.id)
+            } }, collapsed.includes(node.id) || collapsedLeaves.includes(node.id)
             ? 'Show node'
             : 'Hide node')));
 });

package/dist/components/tree/TreeNodeMenu.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TreeNodeMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeNodeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AACnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,SAAS;AACT,MAAM,kBAAkB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,8BAA8B,CAAC,CAAC,CAAA;AAE7E,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAClC,IAAI,EACJ,OAAO,EACP,KAAK,GAKN;IACC,MAAM,EAAE,SAAS,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IAC5C,OAAO,CACL,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;YACd,GAAG,EAAE,IAAI,CAAC,CAAC;YACX,IAAI,EAAE,IAAI,CAAC,CAAC;SACb,EACD,kBAAkB,EAAE,CAAC,EACrB,WAAW,QACX,IAAI,EAAE,OAAO,CAAC,IAAI,CAAC,EACnB,OAAO,EAAE,OAAO;QAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CAAC,IAAI,CACD;QAEX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,kBAAkB;oBAClB;wBACE,IAAI,EAAE,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC;wBACjC,KAAK;wBACL,QAAQ,EAAE,IAAI,CAAC,IAAI;wBACnB,OAAO;qBACR;iBACF,CAAC,CAAA;gBACF,OAAO,EAAE,CAAA;YACX,CAAC,mBAGQ;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC;oBAChC,KAAK,CAAC,eAAe,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAChC,CAAC;qBAAM,CAAC;oBACN,IAAI,IAAI,CAAC,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE,CAAC;wBAClC,KAAK,CAAC,gBAAgB,CAAC,GAAG,IAAI,CAAC,EAAE,EAAE,CAAC,CAAA;oBACtC,CAAC;yBAAM,CAAC;wBACN,KAAK,CAAC,gBAAgB,CAAC,GAAG,IAAI,CAAC,EAAE,WAAW,CAAC,CAAA;oBAC/C,CAAC;gBACH,CAAC;gBACD,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,eAAe,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/D,CAAC,CAAC,WAAW;YACb,CAAC,CAAC,WAAW,CACN,CACN,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

package/dist/components/tree/TreePanel.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const TreePanel: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/tree/TreeRuler.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const TreeRuler: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/tree/dialogs/TreeNodeInfoDialog.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../../model';
+import type { MsaViewModel } from '../../../model';
 declare const _default: ({ info, model, nodeName, onClose, }: {
     info: Record<string, unknown>;
     model: MsaViewModel;

package/dist/components/tree/renderTreeCanvas.d.ts

@@ -1,6 +1,6 @@
-import RBush from 'rbush';
-import { Theme } from '@mui/material';
-import { MsaViewModel } from '../../model';
+import type RBush from 'rbush';
+import type { Theme } from '@mui/material';
+import type { MsaViewModel } from '../../model';
 export declare const padding = 600;
 interface ClickEntry {
     name: string;

package/dist/components/tree/renderTreeCanvas.js

@@ -8,6 +8,9 @@ export function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, })
     ctx.strokeStyle = theme.palette.text.primary;
     for (const link of hierarchy.links()) {
         const { source, target } = link;
+        if (target.height === 0 && !showBranchLen) {
+            continue;
+        }
         const sy = source.x;
         const ty = target.x;
         // @ts-expect-error
@@ -36,9 +39,8 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
         // @ts-expect-error
         const { [val]: x, data } = node;
         const y = node.x;
-        const { branchset, id = '', name = '' } = data;
-        if (!id.endsWith('-leafnode') &&
-            branchset.length &&
+        const { id = '', name = '' } = data;
+        if (node.height > 1 &&
             y > offsetY - extendBounds &&
             y < offsetY + by + extendBounds) {
             ctx.strokeStyle = 'black';
@@ -60,7 +62,10 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
     }
 }
 export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }) {
-    const { fontSize, showBranchLen, treeMetadata, hierarchy, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, noTree, } = model;
+    const { fontSize, showBranchLen, treeMetadata, hierarchy, collapsed, collapsedLeaves, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, 
+    // eslint-disable-next-line  @typescript-eslint/no-unused-vars
+    rowHeight: _rowHeight, // this is needed for redrawing after zoom change
+     } = model;
     const by = blockSizeYOverride || blockSize;
     if (labelsAlignRight) {
         ctx.textAlign = 'right';
@@ -69,7 +74,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
     else {
         ctx.textAlign = 'start';
     }
-    for (const node of hierarchy.leaves()) {
+    for (const node of leaves) {
         const { data: { name, id }, 
         // @ts-expect-error
         len, } = node;
@@ -79,7 +84,16 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
         if (y > offsetY - extendBounds && y < offsetY + by + extendBounds) {
             // note: +rowHeight/4 matches with -rowHeight/4 in msa
             const yp = y + fontSize / 4;
-            const xp = (showBranchLen ? len : x) || 0;
+            let xp = (showBranchLen ? len : x) || 0;
+            if (!showBranchLen &&
+                !collapsed.includes(id) &&
+                !collapsedLeaves.includes(id)) {
+                // this subtraction is a hack to compensate for the leafnode rendering
+                // glitch (issue #71). the context is that an extra leaf node is added
+                // so that 'collapsing/hiding leaf nodes is possible' but this causes
+                // weird workarounds
+                xp -= treeWidth / hierarchy.height;
+            }
             const { width } = ctx.measureText(displayName);
             const height = ctx.measureText('M').width; // use an 'em' for height
             ctx.fillStyle = theme.palette.text.primary;
@@ -119,7 +133,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
 }
 export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }) {
     clickMap?.clear();
-    const { noTree, drawTree, drawLabels, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, fontSize, rowHeight, marginLeft, nref, } = model;
+    const { noTree, drawTree, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, fontSize, showTreeText, marginLeft, nref, } = model;
     const by = blockSizeYOverride || blockSize;
     ctx.resetTransform();
     // this is a bogus use of nref, it is never less than 0. we just are using it
@@ -127,7 +141,9 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
     // just need to use nref to indicate a redraw in an autorun when canvas ref
     // is updated and in order to convince bundlers like not to delete unused
     // usage with propertyReadSideEffects
-    const k = nref < 0 ? -Infinity : highResScaleFactorOverride || highResScaleFactor;
+    const k = nref < 0
+        ? Number.NEGATIVE_INFINITY
+        : highResScaleFactorOverride || highResScaleFactor;
     ctx.scale(k, k);
     ctx.clearRect(0, 0, treeWidth + padding, by);
     ctx.translate(marginLeft, -offsetY);
@@ -152,7 +168,7 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
             });
         }
     }
-    if (rowHeight >= 5 && drawLabels) {
+    if (showTreeText) {
         renderTreeLabels({
             ctx,
             offsetY,

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package/dist/components/util.js

@@ -6,7 +6,7 @@
 export function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     scale = Math.abs(scale);
     const minMajorPitchBp = minMajorPitchPx * scale;
-    const majorMagnitude = parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
+    const majorMagnitude = Number.parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
     let majorPitch = 10 ** majorMagnitude;
     while (majorPitch < minMajorPitchBp) {
         majorPitch *= 2;

package/dist/components/util.js.map

@@ -1 +1 @@
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package/dist/launchInterProScan.d.ts

@@ -1,4 +1,4 @@
-import { MsaViewModel } from './model';
+import type { MsaViewModel } from './model';
 export interface InterProScanResults {
     matches: {
         signature: {

package/dist/launchInterProScan.js

@@ -1,6 +1,6 @@
 import { getSession } from '@jbrowse/core/util';
 import { jsonfetch, textfetch, timeout } from './fetchUtils';
-const base = `https://www.ebi.ac.uk/Tools/services/rest`;
+const base = 'https://www.ebi.ac.uk/Tools/services/rest';
 async function runInterProScan({ seq, onProgress, onJobId, programs, model, }) {
     const jobId = await textfetch(`${base}/iprscan5/run`, {
         method: 'POST',
@@ -23,7 +23,6 @@ export function loadInterProScanResults(jobId) {
 async function wait({ onProgress, jobId, }) {
     const url = `${base}/iprscan5/status/${jobId}`;
     try {
-        // eslint-disable-next-line no-constant-condition
         while (true) {
             for (let i = 0; i < 10; i++) {
                 await timeout(1000);
@@ -33,6 +32,9 @@ async function wait({ onProgress, jobId, }) {
             if (result.includes('FINISHED')) {
                 break;
             }
+            if (result.includes('FAILURE')) {
+                throw new Error(`Failed to run: jobId ${jobId}`);
+            }
         }
     }
     finally {
@@ -52,9 +54,7 @@ export async function launchInterProScan({ algorithm, seq, programs, onJobId, on
             });
             return result;
         }
-        else {
-            throw new Error('unknown algorithm');
-        }
+        throw new Error('unknown algorithm');
     }
     finally {
         onProgress();
@@ -63,13 +63,11 @@ export async function launchInterProScan({ algorithm, seq, programs, onJobId, on
 export async function loadInterProScanResultsWithStatus({ jobId, model, }) {
     try {
         model.setStatus({
-            msg: 'Downloading results of ' +
-                jobId +
-                ' (for larger sequences this can be slow, click status to download and upload in the manual tab)',
+            msg: `Downloading results of ${jobId} (for larger sequences this can be slow, click status to download and upload in the manual tab)`,
             url: `https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/${jobId}/json`,
         });
         const ret = await loadInterProScanResults(jobId);
-        model.setLoadedInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
+        model.setInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
         model.setShowDomains(true);
         getSession(model).notify(`Loaded interproscan ${jobId} results`, 'success');
     }

package/dist/launchInterProScan.js.map

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